US20210154190A1 - Shp2 inhibitor compositions and methods for treating cancer - Google Patents

Shp2 inhibitor compositions and methods for treating cancer Download PDF

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US20210154190A1
US20210154190A1 US17/064,317 US202017064317A US2021154190A1 US 20210154190 A1 US20210154190 A1 US 20210154190A1 US 202017064317 A US202017064317 A US 202017064317A US 2021154190 A1 US2021154190 A1 US 2021154190A1
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shp2
cancer
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David E. Wildes
Carlos Stahlhut-Espinosa
Robert J. Nichols
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Revolution Medicines Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/506—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4965—Non-condensed pyrazines
    • A61K31/497—Non-condensed pyrazines containing further heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4965—Non-condensed pyrazines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/517—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/55—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/55—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole
    • A61K31/551—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole having two nitrogen atoms, e.g. dilazep
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present disclosure relates to methods for the treatment of diseases or disorders (e.g., cancer or an inherited developmental disorder) with inhibitors of the protein tyrosine phosphatase SHP2.
  • diseases or disorders e.g., cancer or an inherited developmental disorder
  • this invention is concerned with methods of treating diseases or disorders (such as cancer or inherited developmental disorder) in subjects that are identified as candidates for treatment with an allosteric SHP2 inhibitor.
  • SHP2 is a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene that contributes to multiple cellular functions including proliferation, differentiation, cell cycle maintenance and migration. SHP2 is involved in signaling through the RAS-mitogen-activated protein kinase (MAPK), the JAK-STAT and/or the phosphoinositol 3-kinase-AKT pathways.
  • MAPK RAS-mitogen-activated protein kinase
  • JAK-STAT the JAK-STAT
  • phosphoinositol 3-kinase-AKT phosphoinositol 3-kinase-AKT pathways.
  • SHP2 has two N-terminal Src homology 2 domains (N—SH2 and C—SH2), a catalytic domain (PTP), and a C-terminal tail.
  • the two SH2 domains control the subcellular localization and functional regulation of SHP2.
  • the molecule exists in an inactive, self-inhibited conformation stabilized by a binding network involving residues from both the N—SH2 and PTP domains. Stimulation by, for example, cytokines or growth factors acting through RTKs leads to exposure of the catalytic site resulting in enzymatic activation of SHP2.
  • Mutations in the PTPN11 gene and subsequently in SHP2 have been identified in several human developmental diseases, such as Noonan Syndrome and LEOPARD Syndrome, as well as human cancers, such as juvenile myelomonocytic leukemias, neuroblastoma, melanoma, acute myeloid leukemia and cancers of the breast, lung and colon. Some of these mutations destabilize the autoinhibited conformation of SHP2 and promote autoactivation or enhanced growth factor-driven activation of SHP2.
  • SHP2 therefore, represents a highly attractive target for the development of novel therapies for the treatment of various diseases including cancer.
  • the present disclosure relates to methods of treating diseases or disorders (such as cancer or inherited developmental disorder) in certain subsets of subjects that are determined to be candidates for treatment with an allosteric SHP2 inhibitor.
  • diseases or disorders such as cancer or inherited developmental disorder
  • the disclosure provides a method of treating a subject having a disease or disorder associated with cells containing a mutant SHP2, comprising administering to the subject an allosteric SHP2 inhibitor, wherein the mutant SHP2 comprises an allosteric inhibitor-sensitive mutation.
  • the allosteric inhibitor-sensitive mutation is F285S, L262R, S189A, D61G, E69K, T73I, or Q506P.
  • the cells are negative for an allosteric inhibitor-resistant mutation of SHP2.
  • the allosteric inhibitor-resistant mutation is E76K, P491S, or S502P.
  • the disclosure provides a method of identifying a subject with SHP2 mutations susceptible to a SHP2 inhibitor, comprising genotyping a biological sample from the subject for SHP2 mutations, wherein the subject is identified as susceptible to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-sensitive mutation.
  • the allosteric inhibitor-sensitive mutation is F285S, L262R, S189A, D61G, E69K, T73I, or Q506P.
  • the disclosure provides a method of identifying a subject as resistant to an allosteric SHP2 inhibitor, comprising genotyping a biological sample from the subject for SHP2 mutations, wherein the subject is identified as resistant to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-resistant mutation.
  • the allosteric inhibitor-resistant mutation is E76K, P491S, or S502P.
  • the disclosure provides a diagnostic test for allosteric SHP2 inhibitor sensitivity, comprising a nucleic acid probe specific for an allosteric inhibitor-sensitive mutation of SHP2.
  • the allosteric inhibitor-sensitive mutation is F285S, L262R, S189A, D61G, E69K, T73I, or Q506P.
  • FIG. 1 shows a simple equilibrium model for activation/inhibition by peptide binding, mutation, and inhibitor binding.
  • FIG. 2 shows the potency of each compound to inhibit non-activated mutant SHP2 plotted versus the potency to inhibit wild-type SHP2.
  • FIG. 3 shows the potency of each compound to inhibit peptide-activated mutant SHP2 plotted versus the potency to inhibit peptide-activated wild-type SHP2.
  • FIG. 4 shows negligible shift in potency for inhibition of wild-type SHP2 between non-activated and peptide-activated biochemical experiments.
  • FIG. 5 shows addition of activating peptide (NsCs, 0.5 ⁇ M) had negligible effect on inhibitor potency for WT SHP2 and varying effects on mutants S189A ( FIG. 5A ), F285C ( FIG. 5B ), D61G ( FIG. 5C ), and E76K ( FIG. 5D ).
  • FIG. 6 shows the generation of isogenic cell lines for SHP2 mutants and their use in cellular assays for SHP2 inhibition.
  • FIG. 7 shows EGF-induced pERK activity for various mutant SHP2s at various concentrations of Compound B
  • FIG. 8 shows that biochemical data from activated SHP2 is a better predictor of cellular sensitivity than biochemical data from unactivated SHP2.
  • FIG. 8A depicts biochemical pIC 50 plotted against cellular pIC 50 for activated SHP2.
  • FIG. 8B depicts biochemical pIC 50 plotted against cellular pIC 50 for unactivated SHP2.
  • an element means one element or more than one element.
  • administer refers to either directly administering a disclosed compound or pharmaceutically acceptable salt of the disclosed compound or a composition to a subject, or administering a prodrug derivative or analog of the compound or pharmaceutically acceptable salt of the compound or composition to the subject, which can form an equivalent amount of active compound within the subject's body.
  • carrier encompasses carriers, excipients, and diluents and means a material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting a pharmaceutical agent from one organ, or portion of the body, to another organ, or portion of the body of a subject.
  • RMC-0693943 (abbreviated herein as “RMC-3943”), which has the following structure:
  • RMC-0694550 abbreviated herein as “RMC-4550”
  • Compound C and “Cmp C” are used interchangeably herein to refer to an allosteric SHP2 inhibitor compound of similar structure to Compounds A and B.
  • Compound C is disclosed in PCT/US2017/041577 (WO 2018/013597), incorporated herein by reference in its entirety.
  • SHP099 refers to a SHP2 inhibitor having the following structure:
  • disorder is used in this disclosure to mean, and is used interchangeably with, the terms disease, condition, or illness, unless otherwise indicated.
  • an “effective amount” when used in connection with a compound is an amount effective for treating or preventing a disease or disorder in a subject as described herein.
  • inhibitor means a compound that prevents a biomolecule, (e.g., a protein, nucleic acid) from completing or initiating a reaction.
  • An inhibitor can inhibit a reaction by competitive, uncompetitive, or non-competitive means.
  • Exemplary inhibitors include, but are not limited to, nucleic acids, DNA, RNA, shRNA, siRNA, proteins, protein mimetics, peptides, peptidomimetics, antibodies, small molecules, chemicals, analogs that mimic the binding site of an enzyme, receptor, or other protein, e.g., that is involved in signal transduction, therapeutic agents, pharmaceutical compositions, drugs, and combinations of these.
  • the inhibitor can be nucleic acid molecules including, but not limited to, siRNA that reduce the amount of functional protein in a cell. Accordingly, compounds said to be “capable of inhibiting” a particular protein, e.g., SHP2, comprise any such inhibitor.
  • allosteric inhibitor means a small-molecule compound capable of inhibiting SHP2 through binding to SHP2 at a site other than the active site of the enzyme.
  • exemplary allosteric SHP2 inhibitors disclosed herein include, without limitation: (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an allosteric SHP2 inhibitor compound of any one of Formula I, of Formula II, of Formula III, of Formula I-V1, of Formula I-V2, of Formula I-W, of Formula I-X, of Formula I-Y, of Formula I-Z, of Formula IV, of Formula V, of Formula VI, of Formula IV-X, of Formula IV-Y, of Formula IV-Z, of Formula VII, of Formula VIII, of Formula IX, and of Formula X; (vi) TNO155; (vii) a SHP2 inhibitor disclosed in international PCT application PCT/US2017/041577 (WO2018013597), incorporated herein by reference in its entirety; (
  • modulating includes “increasing,” “enhancing” or “stimulating,” as well as “decreasing” or “reducing,” typically in a statistically significant or a physiologically significant amount as compared to a control.
  • An “increased,” “stimulated” or “enhanced” amount is typically a “statistically significant” amount, and may include an increase that is 1.1, 1.2, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30 or more times (e.g., 500, 1000 times) (including all integers and decimal points in between and above 1, e.g., 1.5, 1.6, 1.7.
  • a “decreased” or “reduced” amount is typically a “statistically significant” amount, and may include a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease in the amount produced by no composition (the absence of an agent or compound) or a control composition, including all integers in between.
  • mutation indicates any modification of a nucleic acid and/or polypeptide which results in an altered nucleic acid or polypeptide.
  • the term “mutation” may include, for example, point mutations, deletions or insertions of single or multiple residues in a polynucleotide, which includes alterations arising within a protein-encoding region of a gene as well as alterations in regions outside of a protein-encoding sequence, such as, but not limited to, regulatory or promoter sequences, as well as amplifications and/or chromosomal breaks or translocations.
  • allosteric inhibitor-sensitive mutation when used in reference to a SHP2 mutation, means a mutation in SHP2 that results in a SHP2 polypeptide that may be modulated by a SHP2 allosteric inhibitor (e.g., any one of the SHP2 allosteric inhibitors disclosed herein).
  • a SHP2 allosteric inhibitor e.g., any one of the SHP2 allosteric inhibitors disclosed herein.
  • modulation of a SHP2 polypeptide comprising an allosteric inhibitor-sensitive mutation will in some embodiments result in a decrease in the activity of the SHP2 polypeptide.
  • Such activity may be measured using any suitable activity assay known in the art or disclosed herein (see, e.g., the SHP2 allosteric inhibition assay described herein in Example 1).
  • the allosteric inhibitor-sensitive mutation is a SHP2 mutation selected from any one of F285S, L262R, S189A, D61G, E69K, T73I, and Q506P. In some embodiments, the allosteric inhibitor-sensitive mutation may be a combination of two or more SHP2 mutations selected from F285S, L262R, S189A, D61G, E69K, T73I, and Q506P.
  • allosteric inhibitor-resistant mutation when used in reference to a SHP2 mutation, means a mutation in SHP2 that renders a SHP2 polypeptide refractory or resistant to inhibition with a SHP2 allosteric inhibitor.
  • an allosteric inhibitor-resistant mutation in a SHP2 polypeptide decreases the inhibitory effect that a SHP2 allosteric inhibitor has on the SHP2 polypeptide as compared to the effect the inhibitor has on a similar SHP2 polypeptide differing only in the absence of the allosteric inhibitor-resistant mutation.
  • an allosteric inhibitor-resistant mutation in a SHP2 polypeptide abolishes all detectable inhibitory effects that a SHP2 allosteric inhibitor has on the activity of the SHP2 polypeptide, wherein the inhibitor has detectable inhibitory efficacy on a similar SHP2 polypeptide differing only in the absence of the allosteric inhibitor-resistant mutation.
  • Such allosteric inhibitor-resistant mutations include, without limitation, mutations that destabilize the autoinhibited conformation of SHP2.
  • the allosteric inhibitor-resistant mutation is a SHP2 mutation selected from any one of E76K, P491S, and S502P. In some embodiments, the allosteric inhibitor-resistant mutation is a combination of two or more SHP2 mutations selected from E76K, P491S, and S502P.
  • a “patient” or “subject” is a mammal, e.g., a human, mouse, rat, guinea pig, dog, cat, horse, cow, pig, or non-human primate, such as a monkey, chimpanzee, baboon or rhesus.
  • prevent refers to keeping a disease or disorder from afflicting the subject. Preventing includes prophylactic treatment. For instance, preventing can include administering to the subject a compound disclosed herein before a subject is afflicted with a disease and the administration will keep the subject from being afflicted with the disease.
  • a therapeutic agent e.g., a SHP2 inhibitor
  • administering includes administering such an agent.
  • RAS pathway and “RAS/MAPK pathway” are used interchangeably herein to refer to a signal transduction cascade downstream of various cell surface growth factor receptors in which activation of RAS (and its various isoforms and alleotypes) is a central event that drives a variety of cellular effector events that determine the proliferation, activation, differentiation, mobilization, and other functional properties of the cell.
  • SHP2 conveys positive signals from growth factor receptors to the RAS activation/deactivation cycle, which is modulated by guanine nucleotide exchange factors (GEFs, such as SOS1) that load GTP onto RAS to produce functionally active GTP-bound RAS as well as GTP-accelerating proteins (GAPs, such as NF1) that facilitate termination of the signals by conversion of GTP to GDP.
  • GTP-bound RAS produced by this cycle conveys essential positive signals to a series of serine/threonine kinases including RAF and MAP kinases, from which emanate additional signals to various cellular effector functions.
  • RAS pathway mutation and “RAS/MAPK pathway activating mutation” are used interchangeably herein to refer to a mutation in a gene encoding a protein directly involved in the signaling processes of the RAS/MAPK signaling pathway and/or regulating (either positively or negatively) this signaling pathway that renders the pathway active, wherein such mutation may increase, change or decrease the activity level of said protein.
  • proteins include but are not limited to Ras, Raf, NF1, SOS, and specific isoforms or alleotypes thereof.
  • RTK-driven tumor refers to a tumor comprising a cell with one or more oncogenic mutation of an RTK, or a protein that is part of the RTK signaling complex, that causes high levels RTK signaling. Some such cells may be considered “addicted” to the RTK, and inhibition of RTK signaling leads to simultaneous suppression of downstream pathways, often resulting in cell growth, arrest, and death.
  • RTK-driven tumors include, but are not limited to, non-small cell lung cancers (NSCLCs) with mutations in EGFR or ALK.
  • NSCLCs non-small cell lung cancers
  • SHP2 means “Src Homology 2 domain-containing protein tyrosine phosphatase 2” and is also known as SH-PTP2, SH-PTP3, Syp, PTP1D, PTP2C, SAP-2 or PTPN11. Numbering of SHP2 mutations in the present disclosure is according to Uniprot Isoform 2 (accession number Q06124-2) (SEQ ID NO: 1):
  • AAwt ###AAmut is used to indicate a mutation that results in the wild-type amino acid AAwt at position ### in the polypeptide being replaced with mutant AAmut.
  • a “therapeutic agent” is any substance, e.g., a compound or composition, capable of treating a disease or disorder.
  • therapeutic agents that are useful in connection with the present disclosure include without limitation SHP2 inhibitors, ALK inhibitors, MEK inhibitors, RTK inhibitors (TKIs), and cancer chemotherapeutics. Many such inhibitors are known in the art and are disclosed herein.
  • terapéuticaally effective amount is the amount of the drug, e.g., a SHP2 inhibitor, needed to elicit the desired biological response following administration.
  • treatment refers to improving at least one symptom, pathology or marker of the subject's disease or disorder, either directly or by enhancing the effect of another treatment. Treating includes curing, improving, or at least partially ameliorating the disorder, and may include even minimal changes or improvements in one or more measurable markers of the disease or condition being treated. “Treatment” or “treating” does not necessarily indicate complete eradication or cure of the disease or condition, or associated symptoms thereof.
  • the subject receiving this treatment is any subject in need thereof. Exemplary markers of clinical improvement will be apparent to persons skilled in the art.
  • the present disclosure relates to, inter alia, compositions, methods, and kits for treating or preventing a disease or disorder (e.g., cancer) with a SHP2 inhibitor alone or in combination with another suitable therapeutic agent.
  • a disease or disorder e.g., cancer
  • a SHP2 inhibitor alone or in combination with another suitable therapeutic agent.
  • SHP2 is an important signaling effector molecule for a variety of receptor tyrosine kinases (RTKs), including the receptors of platelet-derived growth factor (PDGFR), fibroblast growth factor (FGFR), and epidermal growth factor (EGFR).
  • RTKs receptor tyrosine kinases
  • PDGFR platelet-derived growth factor
  • FGFR fibroblast growth factor
  • EGFR epidermal growth factor
  • SHP2 is also an important signaling molecule that regulates the activation of the mitogen activated protein (MAP) kinase pathway which can lead to cell transformation, a prerequisite for the development of cancer.
  • MAP mitogen activated protein
  • SHP2 is involved in signaling through the Ras-mitogen-activated protein kinase, the JAK-STAT and/or the phosphoinositol 3-kinase-AKT pathways.
  • SHP2 mediates activation of Erk1 and Erk2 (Erk1/2, Erk) MAP
  • SHP2 has two N-terminal Src homology 2 domains (N—SH2 and C—SH2), a catalytic domain (PTP), and a C-terminal tail.
  • the two SH2 domains control the subcellular localization and functional regulation of SHP2.
  • the molecule exists in an inactive conformation, inhibiting its own activity via a binding network involving residues from both the N—SH2 and PTP domains.
  • SHP2 associates with the RTK signaling apparatus, and this induces a conformational change that results in SHP2 activation.
  • Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and LEOPARD Syndrome and may also be found in multiple cancer types, including most RTK-driven tumors, leukemia, lung and breast cancer, gastric carcinoma, anaplastic large-cell lymphoma, glioblastoma and neuroblastoma.
  • PTPN11 is the first identified proto-oncogene that encodes a tyrosine phosphatase. Blood 109, 862-867 (2007). Matozaki, T., Murata, Y., Saito, Y., Okazawa, H. & Ohnishi, H. Protein tyrosine phosphatase SHP-2: a proto-oncogene product that promotes Ras activation. Cancer Sci. 100, 1786-1793 (2009). Mohi, M. G. & Neel, B. G. The role of Shp2 (PTPN11) in cancer. Curr. Opin. Genet. Dev. 17, 23-30 (2007).) ⁇ stman, A., Hellberg, C. & Böhmer, F. D. Protein-tyrosine phosphatases and cancer. Nat. Rev. Cancer 6, 307-320 (2006).
  • SHP2 plays a role in transducing signals originating from immune checkpoint molecules, including but not limited to programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4).
  • PD-1 programmed cell death protein 1
  • CTL-4 cytotoxic T-lymphocyte-associated protein 4
  • inhibition of SHP2 function may promote activation of immune cells expressing checkpoint molecules, including anti-cancer immune responses.
  • the present disclosure provides a method for patient stratification based upon the presence or absence of a SHP2 mutation or based upon the particular subtype of such a mutation.
  • patient stratification means classifying one or more patient as having a disease or disorder (e.g., cancer) that is either likely or unlikely to be treatable with an allosteric SHP2 inhibitor.
  • Patient stratification may comprise classifying a patient as having a tumor that is sensitive to treatment with an allosteric SHP2 inhibitor.
  • the patient stratification may be based on the presence or absence of a tumor comprising one or more cell containing a SHP2 mutation that renders the mutated SHP2 protein sensitive or resistant to allosteric inhibitors of SHP2.
  • any disease or condition associated with a SHP2 mutation may be identified, assessed, and/or treated according to the present disclosure.
  • the SHP2 mutation leaves the mutated protein sensitive to allosteric inhibitors of SHP2.
  • diseases or conditions comprising SHP2 mutations are known in the art.
  • the present disclosure provides methods for treating a disease or condition selected from, but not limited to, Noonan Syndrome (e.g., Noonan syndrome caused by a mechanism other than a SHP2 mutation), LEOPARD Syndrome (e.g., LEOPARD Syndrome caused by a mechanism other than a SHP2 mutation); tumors of hemopoietic and lymphoid system including myeloproliferative syndromes, myelodysplastic syndromes, and leukemia, e.g., acute myeloid leukemia, and juvenile myelomonocytic leukemias; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer, neuroblastoma, bladder cancer, prostate cancer; glioblastoma; urothelial carcinoma, uterine carcinoma, adenoid and ovarian sereous cystadenocarcinoma, paraganglioma, phaeochromocytoma, pancreatic cancer, adrenocor
  • Noonan Syndrome
  • the methods for treating such diseases or disorders involve administering to a subject an effective amount of a SHP2 inhibitor or a composition (e.g., a pharmaceutical composition) comprising a SHP2 inhibitor.
  • a SHP2 inhibitor or a composition comprising a SHP2 inhibitor.
  • Any compound or substance capable of inhibiting SHP2 may be utilized in application with the present disclosure to inhibit SHP2.
  • Non-limiting examples of such SHP2 inhibitors are known in the art and are disclosed herein.
  • the compositions and methods described herein may utilize one or more SHP2 inhibitor selected from, but not limited to, any SHP2 inhibitor disclosed in Chen, Ying-Nan P et al., 148 Nature Vol 535 7 Jul. 2016, incorporated herein by reference in its entirety, including SHP099, disclosed therein.
  • compositions and methods described herein may utilize one or more SHP2 inhibitor selected from, but not limited to any SHP2 inhibitor disclosed in PCT application PCT/US2017/041577 (WO2018013597), which is incorporated herein by reference in its entirety.
  • the compositions and methods described herein may utilize one or more SHP2 inhibitor selected from, but not limited to any SHP2 inhibitor disclosed in PCT applications PCT/IB2015/050343 (WO2015107493); PCT/IB2015/050344 (WO2015107494); PCT/IB2015/050345 (WO201507495); PCT/IB2016/053548 (WO2016/203404); PCT/IB2016/053549 (WO2016203405); PCT/IB2016/053550 (WO2016203406); PCT/US2010/045817 (WO2011022440); PCT/US2017/021784 (WO2017156397); and PCT/US2016/060787 (WO2017079723); and PCT/CN2017/08
  • compositions and methods described herein may utilize one or more SHP2 inhibitor selected from, but not limited to any SHP2 inhibitor disclosed in Chen L, et al., Mol Pharmacol. 2006 August; 70(2):562-70, incorporated herein by reference in its entirety, including NSC-87877 disclosed therein.
  • SHP2 inhibitor selected from, but not limited to any SHP2 inhibitor disclosed in Chen L, et al., Mol Pharmacol. 2006 August; 70(2):562-70, incorporated herein by reference in its entirety, including NSC-87877 disclosed therein.
  • the compositions and methods described herein may utilize TNO155, described under ClinicalTrials.gov Identifier: NCT03114319, available at world wide web address: clinicaltrials.gov/ct2/show/NCT03114319, incorporated herein by reference in its entirety.
  • compositions and methods described herein may utilize one or more SHP2 inhibitor selected from, but not limited to RMC-3943, disclosed herein; RMC-4550, disclosed herein; a SHP2 inhibitor compound of Formula I, Formula II, Formula III, Formula I-VI, Formula I-V2, Formula I-W, Formula I-X, Formula I-Y, Formula I-Z, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X, disclosed herein; a compound from Table A1, disclosed herein; and a compound from Table A2, disclosed herein.
  • SHP2 inhibitor selected from, but not limited to RMC-3943, disclosed herein; RMC-4550, disclosed herein; a SHP2 inhibitor compound of Formula I, Formula II, Formula III, Formula I-VI, Formula I-V2, Formula I-W, Formula I-X, Formula I-Y, Formula I-Z, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S— or a direct bond
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a ), —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )O—,
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —C 1 -C 6 alkyl or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a ), —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )O—,
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —C 1 -C 6 alkyl or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )—
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —C 1 -C 6 alkyl or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl are 5- to 12-membered monocyclic or 5- to 12-membered polycyclic;
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • Y 2 is —NR a —, wherein the bond on the left side of Y 2 , as drawn, is bound to the pyrazine ring and the bond on the right side of the Y 2 moiety, as drawn, is bound to R 3 ;
  • R a and R 4 together with the atom or atoms to which they are attached, are combined to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, —OR 6 , halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 ,
  • R 2 is independently —NH 2 , —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, halogen, —C(O)OR b , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 ,
  • R b is independently, at each occurrence, —H, -D, —OH, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, —(CH 2 ) n -aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, heterocycle, heteroaryl, or —(CH 2 )n-aryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —
  • R 3 is independently —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, a 5- to 12-membered spiroheterocycle, —C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R b , wherein each alkyl, spiroheterocycle, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR b , —NHR b , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , —CF 3 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OR, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN; and
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl are 5- to 12-membered monocyclic or 5- to 12-membered polycyclic;
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • Y 2 is —NR a —, wherein the bond on the left side of Y 2 , as drawn, is bound to the pyrazine ring and the bond on the right side of the Y 2 moiety, as drawn, is bound to R 3 ;
  • R 3 is combined with R a to form a 3- to 12-membered polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, halogen, —OH, —OR b , —NH 2 , —NHR b , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —(CH 2 ) n OH, —COOR b , —CONHR b , —CONH(CH 2 ) n COOR b , —NHCOOR b , —CF 3 , —CHF 2 , —CH 2 F, or ⁇ O;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, —OR 6 , halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 ,
  • R 2 is independently —NH 2 , —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, halogen, —C(O)OR b , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 ,
  • R b is independently, at each occurrence, —H, -D, —OH, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, —(CH 2 )n-aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, heterocycle, heteroaryl, or —(CH 2 )n-aryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5
  • R 4 is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 haloalkyl, —C 1 -C 6 hydroxyalkyl, —CF 2 OH, —CHFOH, —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , —NH 2 , —OH, —CN, —C(O)NR
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , —CF 3 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OR, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN; and
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl are 5- to 12-membered monocyclic or 5- to 12-membered polycyclic;
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a ), —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )O—,
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, —OR 6 , halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, halogen, —C(O)OR b , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, —C 1 -C 6 alkyl, 3- to 12-membered heterocyclyl, or —(CH 2 ) n -aryl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , or wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —OH, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, —(CH 2 )n-aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, heterocycle, heteroaryl, or —(CH 2 )n-aryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5
  • R 3 is independently —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, a 5- to 12-membered spiroheterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R b , wherein each alkyl, spiroheterocycle, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR b , —NHR b , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, halogen, —OH, —OR b , —NH 2 , —NHR b , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —(CH 2 ) n OH, —COOR b , —CONHR b , —CONH(CH 2 ) n COOR b , —NHCOOR b , —CF 3 , —CHF 2 , —CH 2 F, or ⁇ O;
  • R 4 is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 haloalkyl, —C 1 -C 6 hydroxyalkyl —CF 2 OH, —CHFOH —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , —NH 2 , —OH, —CN, —C(O)NR 5 R
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , —CF 3 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OR, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S— or a direct bond
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a ), —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )O—,
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —H, —C 1 -C 6 alkyl, or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently —H, -D, —C 1 -C 6 alkyl, —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —C(O)NR 5 R 6 , —S(O) 2 NR 5 R 6 , C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, wherein each alkyl, cycloalkyl, or heterocyclyl is optionally substituted with one
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S— or a direct bond
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a ), —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)N(R a )O—,
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2
  • R a is independently, at each occurrence, —H, -D, —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR b , —NHR b , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR b , —CONHR b , —CONH(CH 2 ) n COOR b , —NHCOOR b , —CF 3 , —CHF 2 , or —CH 2 F;
  • R 4 is independently —H, -D, —C 1 -C 6 alkyl, —NH—NHR 5 , —NH—OR b , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , —NH 2 , —OH, —CN, —C(O)NR 5 R 6 , —S(O) 2 NR 5 R 6 , C 3 -C 8 cycloalkyl, aryl, heterocyclyl
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is a 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • Y 2 is —NR a —, —(CR a 2 ) m —, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)—, or —C(S)N(R a )—; wherein the bond on the left side of Y 2 , as
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —NH 2 , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, halogen, —C(O)OR b , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 ,
  • R a is independently, at each occurrence —OH, —C 3 -C 8 cycloalkyl, or —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 3 -C 8 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, and O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 R
  • R 3 is independently —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR b , —NHR b , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR b , —CONHR b , —CONH(CH 2 ) n COOR b , —NHCOOR b , —CF 3 , —CHF 2 , or —CH 2 F;
  • R 4 is independently —C 1 -C 6 alkyl, —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , —NH 2 , —OH, —C(O)NR 5 R 6 , —S(O) 2 NR 5 R 6 , C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of
  • R a and R 4 together with the atom or atoms to which they are attached, are combined to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , or —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently, at each occurrence, 1, 2, 3, 4, 5 or 6;
  • n is independently, at each occurrence, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • One aspect of the invention relates to compounds of Formula IV:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S— or a direct bond
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently, at each occurrence, —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Another aspect of the invention relates to compounds of Formula V:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S
  • R 3 is independently, at each occurrence, selected from the group consisting of —C 1 -C 6 alkyl, or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently, at each occurrence, —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S
  • R 3 is independently, at each occurrence, selected from the group consisting of —C 1 -C 6 alkyl, or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, or —NH 2 ; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, or —NH 2 ;
  • R 4 is independently, at each occurrence, —H, -D, or —C 1 -C 6 alkyl, wherein each alkyl is optionally substituted with one or more —OH, —NH 2 , halogen, or oxo; or
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • One aspect of the invention relates to compounds of Formula IV-Y:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S— or a direct bond
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —NR 5 S(O)NR 5 R 6 ,
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 4 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , NH 2 , —OH, —CN, —C(O)NR 5 R 6 , —S(O) 2 NR 5 R 6 , C 3 -C 8 cycloalkyl, aryl, hetero
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • One aspect of the invention relates to compounds of Formula IV-Z:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • R 2 is independently —OR b , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —NH 2 , halogen, —C(O)OR a , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 ,
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —NR 5 S(O)NR 5 R 6 ,
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 4 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —NH—NHR 5 , —NH—OR 5 , —O—NR 5 R 6 , —NHR 5 , —OR 5 , —NHC(O)R 5 , —NHC(O)NHR 5 , —NHS(O) 2 R 5 , —NHS(O) 2 NHR 5 , —S(O) 20 H, —C(O)OR 5 , —NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n OH, —C(O)NH(CH 2 ) n R b , —C(O)R b , NH 2 , —OH, —CN, —C(O)NR 5 R 6 , —S(O) 2 NR 5 R 6 , C 3 -C 8 cycloalkyl, aryl, hetero
  • R a and R 4 together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C 3 -C 12 cycloalkyl, or a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein the cycloalkyl or heterocycle is optionally substituted with oxo; wherein the heterocycle optionally comprises —S(O) 2 — in the heterocycle;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 ,
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • One aspect of the invention relates to compounds of Formula VII:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • X 1 is N or C
  • X 2 is N or CH
  • B including the atoms at the points of attachment, is a monocyclic or polycyclic 5- to 12-membered heterocycle or a monocyclic or polycyclic 5- to 12-membered heteroaryl;
  • R 2 is independently H, —OR b , —NR 5 R 6 , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —NH 2 , halogen, —C(O)OR a , —C 3 -C 8 cycloalkyl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —NR 5 S(O)NR 5 R 6 ,
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • Y 1 is —S—, a direct bond, —NH—, —S(O) 2 —, —S(O) 2 —NH—, —C( ⁇ CH 2 )—, —CH—, or —S(O)—;
  • X 1 is N or C
  • X 2 is N or CH
  • B including the atoms at the points of attachment, is a monocyclic or polycyclic 5- to 12-membered heterocycle or a monocyclic or polycyclic 5- to 12-membered heteroaryl;
  • R 2 is independently H, —OR b , —NR 5 R 6 , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —NH 2 , halogen, —C(O)OR a , —C 3 -C 8 cycloalkyl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • X 1 is N or C
  • X 2 is N or CH
  • B including the atoms at the points of attachment, is a monocyclic or polycyclic 5- to 12-membered heterocycle or a monocyclic or polycyclic 5- to 12-membered heteroaryl;
  • R 2 is independently H, —OR b , —NR 5 R 6 , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —NH 2 , halogen, —C(O)OR a , —C 3 -C 8 cycloalkyl, aryl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —R 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —NR 5 S(O)NR 5 R 6 ,
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R, wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Another aspect of the invention relates to compounds of Formula X:
  • A is selected from the group consisting of 5- to 12-membered monocyclic or polycyclic cycloalkyl, heterocycloalkyl, aryl, or heteroaryl;
  • R 1 is independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, —OH, halogen, —NO 2 , —CN, —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S(O)NR 5 R 6 , —NR 5 S(O)R 6 , —C(O)R 5 , or —CO 2 R 5 ,
  • X 1 is N or C
  • X 2 is N or CH
  • B including the atoms at the points of attachment, is a monocyclic or polycyclic 5- to 12-membered heterocycle or a monocyclic or polycyclic 5- to 12-membered heteroaryl;
  • R 2 is independently H, —OR b , —NR 5 R 6 , —CN, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —NH 2 , halogen, —C(O)OR a , —C 3 -C 8 cycloalkyl, heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, or heteroaryl is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5
  • Y 2 is selected from the group consisting of: —NR a —, —(CR a 2 ) m —, —C(O)—, —C(R a ) 2 NH—, —(CR a 2 ) m O—, —C(O)N(R a )—, —N(R a )C(O)—, —S(O) 2 N(R a )—, —N(R a )S(O) 2 —, —N(R a )C(O)N(R a )—, —N(R a )C(S)N(R a )—, —C(O)O—, —OC(O)—, —OC(O)N(R a )—, —N(R a )C(O)O—, —C(O)N(R a )O—, —N(R a )C(S)
  • R a is independently, at each occurrence, selected from the group consisting of —H, -D, —OH, —C 3 -C 8 cycloalkyl, and —C 1 -C 6 alkyl, wherein each alkyl or cycloalkyl is optionally substituted with one or more —NH 2 , wherein 2 R a , together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl;
  • R b is independently —H, -D, —C 1 -C 6 alkyl, —C 1 -C 6 cycloalkyl, —C 2 -C 6 alkenyl, or heterocyclyl containing 1-5 heteroatoms selected from the group consisting of N, S, P, or O; wherein each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted with one or more —OH, halogen, —NO 2 , oxo, —CN, —R 5 , —OR 5 , —NR 5 R 6 , —SR 5 , —S(O) 2 NR 5 R 6 , —S(O) 2 R 5 , —NR 5 S(O) 2 NR 5 R 6 , —NR 5 S(O) 2 R 6 , —S(O)NR 5 R 6 , —S(O)NR 5 R 6 , —S(O)R 5 , —NR 5 S
  • R 3 is independently, at each occurrence, selected from the group consisting of —H, —C 1 -C 6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, C 3 -C 8 cycloalkyl, or —(CH 2 ) n —R b , wherein each alkyl, heterocycle, or cycloalkyl is optionally substituted with one or more —C 1 -C 6 alkyl, —OH, —NH 2 , —OR a , —NHR a , —(CH 2 ) n OH, heterocyclyl, or spiroheterocyclyl; or
  • R 3 can combine with R a to form a 3- to 12-membered monocyclic or polycyclic heterocycle, or a 5- to 12-membered spiroheterocycle, wherein each heterocycle or spiroheterocycle is optionally substituted with —C 1 -C 6 alkyl, —OH, —NH 2 , heteroaryl, heterocyclyl, —(CH 2 ) n NH 2 , —COOR a , —CONHR b , —CONH(CH 2 ) n COOR a , —NHCOOR a , —CF 3 , CHF 2 , or CH 2 F;
  • R 5 and R 6 are each independently, at each occurrence, selected from the group consisting of —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, —OR 7 , —SR 7 , halogen, —NR 7 R 8 , —NO 2 , and —CN;
  • R 7 and R 8 are independently, at each occurrence, —H, -D, —C 1 -C 6 alkyl, —C 2 -C 6 alkenyl, —C 4 -C 8 cycloalkenyl, —C 2 -C 6 alkynyl, —C 3 -C 8 cycloalkyl, a monocyclic or polycyclic 3- to 12-membered heterocycle, wherein each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted with one or more —OH, —SH, —NH 2 , —NO 2 , or —CN;
  • n is independently 1, 2, 3, 4, 5 or 6;
  • n is independently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Another aspect of the present disclosure relates to compounds, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, or isomers thereof, in Table A1.
  • Another aspect of the present disclosure relates to compounds, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, or isomers thereof, in Table A2.
  • aryl refers to cyclic, aromatic hydrocarbon groups that have 1 to 2 aromatic rings, including monocyclic or bicyclic groups such as phenyl, biphenyl or naphthyl. Where containing two aromatic rings (bicyclic, etc.), the aromatic rings of the aryl group may be joined at a single point (e.g., biphenyl), or fused (e.g., naphthyl).
  • the aryl group may be optionally substituted by one or more substituents, e.g., 1 to 5 substituents, at any point of attachment.
  • substituents include, but are not limited to, —H, halogen, —O—C-C 6 alkyl, —C 1 -C 6 alkyl, —OC 2 -C 6 alkenyl, —OC 2 -C 6 alkynyl, —C 2 -C 6 alkenyl, —C 2 -C 6 alkynyl, —OH, —OP(O)(OH) 2 , —OC(O)C 1 -C 6 alkyl, —C(O)C 1 -C 6 alkyl, —OC(O)OC 1 -C 6 alkyl, —NH 2 , —NH(C 1 -C 6 alkyl), —N(C 1 -C 6 alkyl) 2 , —S(O) 2 —C 1 -C 6 alkyl, —S(O)NHC 1 -C 6 alkyl, and —S(O)N(C 1 -C 6 alkyl)
  • heteroaryl means a monovalent or multivalent monocyclic aromatic radical or a polycyclic aromatic radical of 5 to 24 ring atoms, containing one or more ring heteroatoms selected from N, S, P, and O, the remaining ring atoms being C.
  • Heteroaryl as herein defined also means a bicyclic heteroaromatic group wherein the heteroatom is selected from N, S, P, and O.
  • the aromatic radical is optionally substituted independently with one or more substituents described herein.
  • Examples include, but are not limited to, furyl, thienyl, pyrrolyl, pyridyl, pyrazolyl, pyrimidinyl, imidazolyl, isoxazolyl, oxazolyl, oxadiazolyl, pyrazinyl, indolyl, thiophen-2-yl, quinolyl, benzopyranyl, isothiazolyl, thiazolyl, thiadiazolyl, benzo[d]imidazolyl, thieno[3,2-b]thiophene, triazolyl, triazinyl, imidazo[1,2-b]pyrazolyl, furo[2,3-c]pyridinyl, imidazo[1,2-a]pyridinyl, indazolyl, 1-methyl-1H-indazolyl, pyrrolo[2,3-c]pyridinyl, pyrrolo[3,2-c]pyridinyl, pyrazol
  • Alkyl refers to a straight or branched chain saturated hydrocarbon.
  • C 1 -C 6 alkyl groups contain 1 to 6 carbon atoms. Examples of a C 1 -C 6 alkyl group include, but are not limited to, methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, sec-butyl and tert-butyl, isopentyl and neopentyl.
  • alkenyl means an aliphatic hydrocarbon group containing a carbon carbon double bond and which may be straight or branched having about 2 to about 6 carbon atoms in the chain. Certain alkenyl groups have 2 to about 4 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl, or propyl are attached to a linear alkenyl chain. Exemplary alkenyl groups include ethenyl, propenyl, n-butenyl, and i-butenyl.
  • a C 2 -C 6 alkenyl group is an alkenyl group containing between 2 and 6 carbon atoms.
  • alkynyl means an aliphatic hydrocarbon group containing a carbon carbon triple bond and which may be straight or branched having about 2 to about 6 carbon atoms in the chain. Certain alkynyl groups have 2 to about 4 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl, or propyl are attached to a linear alkynyl chain. Exemplary alkynyl groups include ethynyl, propynyl, n-butynyl, 2-butynyl, 3-methylbutynyl, and n-pentynyl.
  • a C 2 -C 6 alkynyl group is an alkynyl group containing between 2 and 6 carbon atoms.
  • cycloalkyl means monocyclic or polycyclic saturated carbon rings containing 3-18 carbon atoms.
  • cycloalkyl groups include, without limitations, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptanyl, cyclooctanyl, norboranyl, norborenyl, bicyclo[2.2.2]octanyl, or bicyclo[2.2.2]octenyl.
  • a C 3 -C 8 cycloalkyl is a cycloalkyl group containing between 3 and 8 carbon atoms.
  • a cycloalkyl group can be fused (e.g., decalin) or bridged (e.g., norbornane).
  • cycloalkenyl means monocyclic, non-aromatic unsaturated carbon rings containing 4-18 carbon atoms.
  • examples of cycloalkenyl groups include, without limitation, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl, and norborenyl.
  • a C 4 -C 8 cycloalkenyl is a cycloalkenyl group containing between 4 and 8 carbon atoms.
  • heterocyclyl or “heterocycloalkyl” or “heterocycle” refer to monocyclic or polycyclic 3 to 24-membered rings containing carbon and heteroatoms selected from oxygen, phosphorus, nitrogen, and sulfur and wherein there are no delocalized R electrons (aromaticity) shared among the ring carbon or heteroatoms.
  • Heterocyclyl rings include, but are not limited to, oxetanyl, azetidinyl, tetrahydrofuranyl, pyrrolidinyl, oxazolinyl, oxazolidinyl, thiazolinyl, thiazolidinyl, pyranyl, thiopyranyl, tetrahydropyranyl, dioxalinyl, piperidinyl, morpholinyl, thiomorpholinyl, thiomorpholinyl S-oxide, thiomorpholinyl S-dioxide, piperazinyl, azepinyl, oxepinyl, diazepinyl, tropanyl, and homotropanyl.
  • a heteroycyclyl or heterocycloalkyl ring can also be fused or bridged, e.g., can be a bicyclic ring.
  • heterocyclyl or “heterocycloalkyl” or “heterocycle” is a saturated, partially saturated or unsaturated, mono or bicyclic ring containing 3-24 atoms of which at least one atom is chosen from nitrogen, sulfur or oxygen, which may, unless otherwise specified, be carbon or nitrogen linked, wherein a —CH 2 — group can optionally be replaced by a —C(O)— or a ring sulfur atom may be optionally oxidised to form the S-oxides.
  • Heterocyclyl can be a saturated, partially saturated or unsaturated, mono or bicyclic ring containing 5 or 6 atoms of which at least one atom is chosen from nitrogen, sulfur or oxygen, which may, unless otherwise specified, be carbon or nitrogen linked, wherein a —CH 2 — group can optionally be replaced by a —C(O)— or a ring sulfur atom may be optionally oxidised to form S-oxide(s).
  • heterocyclyl are thiazolidinyl, pyrrolidinyl, pyrrolinyl, 2-pyrrolidonyl, 2,5-dioxopyrrolidinyl, 2-benzoxazolinonyl, 1,1-dioxotetrahydro thienyl, 2,4-dioxoimidazolidinyl, 2-oxo-1,3,4-(4-triazolinyl), 2-oxazolidinonyl, 5,6-dihydro uracilyl, 1,3-benzodioxolyl, 1,2,4-oxadiazolyl, 2-azabicyclo[2.2.1]heptyl, 4-thiazolidonyl, morpholino, 2-oxotetrahydrofuranyl, tetrahydrofuranyl, 2,3-dihydrobenzofuranyl, benzothienyl, tetrahydropyrany
  • halo or halogen means a fluoro, chloro, bromo, or iodo group.
  • carbonyl refers to a functional group comprising a carbon atom double-bonded to an oxygen atom. It can be abbreviated herein as “oxo,” as C(O), or as C ⁇ O.
  • “Spirocycle” or “spirocyclic” means carbogenic bicyclic ring systems with both rings connected through a single atom.
  • the ring can be different in size and nature, or identical in size and nature. Examples include spiropentane, spirohexane, spiroheptane, spirooctane, spirononane, or spirodecane.
  • One or both of the rings in a spirocycle can be fused to another carbocyclic, heterocyclic, aromatic, or heteroaromatic ring.
  • One or more of the carbon atoms in the spirocycle can be substituted with a heteroatom (e.g., O, N, S, or P).
  • a C 5 -C 12 spirocycle is a spirocycle containing between 5 and 12 carbon atoms.
  • a C 5 -C 12 spirocycle is a spirocycle containing from 5 to 12 carbon atoms.
  • One or more of the carbon atoms can be substituted with a heteroatom.
  • spirocyclic heterocycle is understood to mean a spirocycle wherein at least one of the rings is a heterocycle (e.g., at least one of the rings is furanyl, morpholinyl, or piperadinyl).
  • a spirocyclic heterocycle can contain between 5 and 12 atoms, at least one of which is a heteroatom selected from N, O, S and P.
  • a spirocyclic heterocycle can contain from 5 to 12 atoms, at least one of which is a heteroatom selected from N, O, S and P.
  • tautomers refers to a set of compounds that have the same number and type of atoms, but differ in bond connectivity and are in equilibrium with one another.
  • a “tautomer” is a single member of this set of compounds. Typically a single tautomer is drawn but it is understood that this single structure is meant to represent all possible tautomers that might exist. Examples include enol-ketone tautomerism. When a ketone is drawn it is understood that both the enol and ketone forms are part of the disclosure.
  • the SHP2 inhibitor may be administered alone as a monotherapy or in combination with one or more other therapeutic agent (e.g., an inhibitor of a MAP kinase pathway or an anti-cancer therapeutic agent) as a combination therapy.
  • the SHP2 inhibitor may be administered as a pharmaceutical composition.
  • the SHP2 inhibitor may be administered before, after, and/or concurrently with the one or more other therapeutic agent (e.g., an inhibitor of a MAP kinase pathway or an anti-cancer therapeutic agent).
  • such administration may be simultaneous (e.g., in a single composition) or may be via two or more separate compositions, optionally via the same or different modes of administration (e.g., local, systemic, oral, intravenous, etc.).
  • compositions and compounds can be accomplished via any mode of administration for therapeutic agents.
  • modes include systemic or local administration such as oral, nasal, parenteral, transdermal, subcutaneous, vaginal, buccal, rectal or topical administration modes.
  • the disclosed compounds or pharmaceutical compositions can be in solid, semi-solid or liquid dosage form, such as, for example, injectables, tablets, suppositories, pills, time-release capsules, elixirs, tinctures, emulsions, syrups, powders, liquids, suspensions, or the like, sometimes in unit dosages and consistent with conventional pharmaceutical practices.
  • injectables tablets, suppositories, pills, time-release capsules, elixirs, tinctures, emulsions, syrups, powders, liquids, suspensions, or the like, sometimes in unit dosages and consistent with conventional pharmaceutical practices.
  • they can also be administered in intravenous (both bolus and infusion), intraperitoneal, subcutaneous or intramuscular form, and all using forms well known to those skilled in the pharmaceutical arts.
  • compositions suitable for the delivery of a SHP2 inhibitor (alone or, e.g., in combination with another therapeutic agent according to the present disclosure) and methods for their preparation will be readily apparent to those skilled in the art. Such compositions and methods for their preparation may be found, e.g., in Remington's Pharmaceutical Sciences, 19th Edition (Mack Publishing Company, 1995), incorporated herein in its entirety.
  • Illustrative pharmaceutical compositions are tablets and gelatin capsules comprising a SHP2 inhibitor alone or in combination with another therapeutic agent according to the disclosure and a pharmaceutically acceptable carrier, such as a) a diluent, e.g., purified water, triglyceride oils, such as hydrogenated or partially hydrogenated vegetable oil, or mixtures thereof, corn oil, olive oil, sunflower oil, safflower oil, fish oils, such as EPA or DHA, or their esters or triglycerides or mixtures thereof, omega-3 fatty acids or derivatives thereof, lactose, dextrose, sucrose, mannitol, sorbitol, cellulose, sodium, saccharin, glucose and/or glycine; b) a lubricant, e.g., silica, talcum, stearic acid, its magnesium or calcium salt, sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and/
  • Liquid, particularly injectable, compositions can, for example, be prepared by dissolution, dispersion, etc.
  • a SHP2 inhibitor (alone or in combination with another therapeutic agent according to the disclosure) is dissolved in or mixed with a pharmaceutically acceptable solvent such as, for example, water, saline, aqueous dextrose, glycerol, ethanol, and the like, to thereby form an injectable isotonic solution or suspension.
  • a pharmaceutically acceptable solvent such as, for example, water, saline, aqueous dextrose, glycerol, ethanol, and the like.
  • Proteins such as albumin, chylomicron particles, or serum proteins can be used to solubilize the SHP2 inhibitor (alone or in combination with another therapeutic agent according to the disclosure).
  • the SHP2 inhibitor can be also formulated as a suppository, alone or in combination with another therapeutic agent according to the disclosure, which can be prepared from fatty emulsions or suspensions; using polyalkylene glycols such as propylene glycol, as the carrier.
  • the SHP2 inhibitor can also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles and multilamellar vesicles, either alone or in combination with another therapeutic agent according to the disclosure.
  • Liposomes can be formed from a variety of phospholipids, containing cholesterol, stearylamine or phosphatidylcholines.
  • a film of lipid components is hydrated with an aqueous solution of drug to a form lipid layer encapsulating the drug, as described for instance in U.S. Pat. No. 5,262,564, the contents of which are hereby incorporated by reference.
  • SHP2 inhibitors can also be delivered by the use of monoclonal antibodies as individual carriers to which the disclosed compounds are coupled.
  • SHP2 inhibitors can also be coupled with soluble polymers as targetable drug carriers.
  • Such polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacrylamide-phenol, polyhydroxyethylaspanamidephenol, or polyethyleneoxidepolylysine substituted with palmitoyl residues.
  • a SHP2 inhibitor can be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • a polymer e.g., a polycarboxylic acid polymer, or a polyacrylate.
  • Parental injectable administration is generally used for subcutaneous, intramuscular or intravenous injections and infusions.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions or solid forms suitable for dissolving in liquid prior to injection.
  • compositions comprising a SHP2 inhibitor (alone or in combination with another therapeutic agent according to the present disclosure) and a pharmaceutically acceptable carrier.
  • the pharmaceutically acceptable carrier can further include an excipient, diluent, or surfactant.
  • compositions comprising one or more SHP2 inhibitor for use in a method disclosed herein, e.g., a SHP2 monotherapy.
  • Such compositions may comprise a SHP2 inhibitor and, e.g., one or more carrier, excipient, diluent, and/or surfactant.
  • compositions comprising one or more SHP2 inhibitor and one or more additional therapeutic agent for use in a method disclosed herein, e.g., a SHP2 combination therapy.
  • Such compositions may comprise a SHP2 inhibitor, an additional therapeutic agent (e.g., a TKI, a MAPK pathway inhibitor, an EGFR inhibitor, an ALK inhibitor, a MEK inhibitor) and, e.g., one or more carrier, excipient, diluent, and/or surfactant.
  • compositions comprising one or more SHP2 inhibitor and one or more MK inhibitor for use in a method disclosed herein, e.g., a SHP2 combination therapy.
  • Such compositions may comprise a SHP2 inhibitor, a MEK inhibitor and, e.g., one or more carrier, excipient, diluent, and/or surfactant.
  • Such compositions may consist essentially of a SHP2 inhibitor, a MEK inhibitor and, e.g., one or more carrier, excipient, diluent, and/or surfactant.
  • compositions may consist of a SHP2 inhibitor, a MEK inhibitor and, e.g., one or more carrier, excipient, diluent, and/or surfactant.
  • a composition of the present disclosure may comprise, consist essentially of, or consist of (a) a SHP2 inhibitor; (b) a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973/XL581), Binimetinib, Vemurafenib, Pimasertib, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; Refametinib (RDEA 119/BAY 86-9766); RO5126766, AZD8330 (ARRY-424704/ARRY-704); and GSK1120212; and (c) one or more carrier, excipient
  • compositions of the present disclosure may comprise, consist essentially of, or consist of (a) a MEK inhibitor; (b) a SHP2 inhibitor selected from (i) RMC-3943; (ii) RMC-4550; (iii) SHP099; (iv) a SHP2 inhibitor compound of any one of Formula I, of Formula II, of Formula III, of Formula I-V1, of Formula I-V2, of Formula I-W, of Formula I-X, of Formula I-Y, of Formula I-Z, of Formula IV, of Formula V, of Formula VI, of Formula IV-X, of Formula IV-Y, of Formula IV-Z, of Formula VII, of Formula VIII, of Formula IX, and of Formula X; (v) TNO155, (vi) a SHP2 inhibitor disclosed in international PCT application PCT/US2017/041577 (WO2018013597), incorporated herein by reference in its entirety; (vii) Compound C; (ix) a compound from Table A1, disclosed herein; (x)
  • compositions can be prepared according to conventional mixing, granulating or coating methods, respectively, and the present pharmaceutical compositions can contain from about 0.1% to about 99%, from about 5% to about 90%, or from about 1% to about 20% of the disclosed RMC-4550 by weight or volume.
  • the dosage regimen utilizing the disclosed compound is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal or hepatic function of the patient; and the particular disclosed compound employed.
  • a physician or veterinarian of ordinary skill in the art can readily determine and prescribe the effective amount of the drug required to prevent, counter or arrest the progress of the condition.
  • Effective dosage amounts of a SHP2 inhibitor when used for the indicated effects, range from about 0.5 mg to about 5000 mg as needed to treat the condition.
  • Compositions for in vivo or in vitro use can contain about 0.5, 5, 20, 50, 75, 100, 150, 250, 500, 750, 1000, 1250, 2500, 3500, or 5000 mg of the disclosed compound, or, in a range of from one amount to another amount in the list of doses.
  • the compositions are in the form of a tablet that can be scored.
  • the means for determine comprises a means for determining whether the sample comprises any of an allosteric inhibitor-resistant mutation to SHP2.
  • the means for determine comprises a means for determining whether the sample comprises any of an allosteric inhibitor-sensitive mutation to SHP2.
  • the means for determine comprises a means for determining whether the sample comprises any of the following mutations to SHP2: F285S, L262R, S189A, D61G, E69K, T73I, Q506P, E76K, P491S, or S502P.
  • Such means include, but are not limited to direct sequencing, and utilization of a high-sensitivity diagnostic assay (with CE-IVD mark), e.g., as described in Domagala, et al., Pol J Pathol 3: 145-164 (2012), incorporated herein by reference in its entirety, including TheraScreen PCR; AmoyDx; PNAClamp; RealQuality; EntroGen; LightMix; StripAssay; Hybcell plexA; Devyser; Surveyor; Cobas; and TheraScreen Pyro.
  • a high-sensitivity diagnostic assay with CE-IVD mark
  • Example Embodiment I As follows:
  • Example Embodiment I-1 A method of treating a subject having a disease or disorder associated with cells containing a mutant SHP2, comprising administering to the subject an allosteric SHP2 inhibitor, wherein the mutant SHP2 comprises an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-1a An allosteric SHP2 inhibitor for use in a method of treating a subject having a disease or disorder associated with cells containing a mutant SHP2, wherein the mutant SHP2 comprises an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-1b Use of an allosteric SHP2 inhibitor for the manufacture of a medicament for treating a subject having a disease or disorder associated with cells containing a mutant SHP2, wherein the mutant SHP2 comprises an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-2a The method of Example Embodiment I-1, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, S189A, D61G, E69K, T73I, Q506P, and a combination thereof.
  • Example Embodiment I-2b The method of Example Embodiment I-1, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, and S189A.
  • Example Embodiment I-3 The method of Example Embodiment I-1, wherein the allosteric inhibitor-sensitive mutation is D61G.
  • Example Embodiment I-4 The method of Example Embodiment I-1, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of E69K, T73I, and Q506P.
  • Example Embodiment I-5 The method of any one of the preceding Example Embodiments, wherein the cells are negative for an allosteric inhibitor-resistant mutation of SHP2.
  • Example Embodiment I-6a The method of Example Embodiment I-5, wherein the allosteric inhibitor-resistant mutation is selected from the group consisting of E76K, P491S, S502P, and a combination thereof.
  • Example Embodiment I-6b The method of Example Embodiment I-5, wherein the allosteric inhibitor-resistant mutation is selected from the group consisting of E76K and P491S
  • Example Embodiment I-7 The method of Example Embodiment I-5, wherein the allosteric inhibitor-resistant mutation is S502P.
  • Example Embodiment I-8 The method of any one of the preceding Example Embodiments, wherein the cells are determined to have the allosteric inhibitor-sensitive mutation prior to administering the SHP2 inhibitor.
  • Example Embodiment I-9 The method of any one of the preceding Example Embodiments, wherein the cells are determined to not have the allosteric inhibitor-resistant mutation prior to administering the SHP2 inhibitor.
  • Example Embodiment I-10 The method of any one of the preceding Example Embodiments, wherein the allosteric SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an allosteric SHP2 inhibitor compound of any one of Formula I, of Formula II, of Formula III, of Formula I-V1, of Formula I-V2, of Formula I-W, of Formula I-X, of Formula I-Y, of Formula I-Z, of Formula IV, of Formula V, of Formula VI, of Formula IV-X, of Formula IV-Y, of Formula IV-Z, of Formula VII, of Formula VIII, of Formula IX, and of Formula X; (vi) TNO155; (vii) a SHP2 inhibitor disclosed in international PCT application PCT/US2017/041577 (W2018013597), incorporated herein by reference in its entirety; (viii) a compound from Table A1, disclosed herein; (ix) a compound from Table A2,
  • Example Embodiment I-11 The method of any one of the preceding Example Embodiments, wherein the disease or disorder is selected from tumors of hemopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndromes; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian sereous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinoma; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (e.g.,
  • Example Embodiment I-12 The method of any one of the preceding Example Embodiments, wherein the disease or disorder is an inherited developmental disorder selected from the group consisting of Noonan Syndrome and LEOPARD Syndrome.
  • Example Embodiment I-13 The method of any one of any one of the preceding Example Embodiments, wherein the allosteric SHP2 inhibitor is administered in an effective amount.
  • Example Embodiment I-14 A method of identifying a subject with SHP2 mutations susceptible to a SHP2 inhibitor, comprising genotyping a biological sample from the subject for SHP2 mutations, wherein the subject is identified as susceptible to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-14a An in vitro method of identifying a subject with SHP2 mutations susceptible to a SHP2 inhibitor, comprising genotyping, via an in vitro assay, a biological sample from the subject for SHP2 mutations, wherein the subject is identified as susceptible to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-14b An allosteric SHP2 inhibitor for use in a method of treating a subject identified by genotyping as having a disease or disorder with a SHP2 mutation that is susceptible to a SHP2 inhibitor, wherein the subject is identified as susceptible to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-14c Use of an allosteric SHP2 inhibitor for the manufacture of a medicament for treating a subject identified by genotyping as having a disease or disorder with a SHP2 mutation that is susceptible to a SHP2 inhibitor, wherein the subject is identified as susceptible to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-sensitive mutation.
  • Example Embodiment I-15a The method of Example Embodiment I-14, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, S189A, D61G, E69K, T73I, Q506P, and a combination thereof.
  • Example Embodiment I-15b The method of Example Embodiment I-14, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, and S189A.
  • Example Embodiment I-16 The method of Example Embodiment I-14, wherein the allosteric inhibitor-sensitive mutation is D61G.
  • Example Embodiment I-17 The method of Example Embodiment I-14, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of E69K, T73I, and Q506P.
  • Example Embodiment I-18 The method of any one of Example Embodiments I-14 to I-15, wherein the method further comprises identifying the subject as not expressing a SHP2 allosteric inhibitor-resistant mutation.
  • Example Embodiment I-19 The method of Example Embodiment I-18, wherein the SHP2 allosteric inhibitor-resistant mutation is selected from the group consisting of E76K, P491S, S502P, and a combination thereof.
  • Example Embodiment I-20 The method of Example Embodiment I-18, wherein the allosteric inhibitor-resistant mutation is selected from the group consisting of E76K and P491S
  • Example Embodiment I-21 The method of Example Embodiment I-18, wherein the allosteric inhibitor-resistant mutation is S502P.
  • Example Embodiment I-22 The method of any one of Example Embodiments I-14 to I-21, wherein the allosteric SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an allosteric SHP2 inhibitor compound of any one of Formula I, of Formula II, of Formula III, of Formula I-V1, of Formula I-V2, of Formula I-W, of Formula I-X, of Formula I-Y, of Formula I-Z, of Formula IV, of Formula V, of Formula VI, of Formula IV-X, of Formula IV-Y, of Formula IV-Z, of Formula VII, of Formula VIII, of Formula IX, and of Formula X; (vi) TNO155, and (vii) a combination thereof.
  • the allosteric SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an alloster
  • Example Embodiment I-23 The method of any one of Example Embodiments I-14 through I-22, wherein the allosteric SHP2 inhibitor is in an effective amount.
  • Example Embodiment I-24 A method of identifying a subject as resistant to an allosteric SHP2 inhibitor, comprising genotyping a biological sample from the subject for SHP2 mutations, wherein the subject is identified as resistant to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-resistant mutation.
  • Example Embodiment I-24a An in vitro method of identifying a subject as resistant to an allosteric SHP2 inhibitor, comprising genotyping, via an in vitro assay, a biological sample from the subject for SHP2 mutations, wherein the subject is identified as resistant to the SHP2 inhibitor if the SHP2 mutations comprise an allosteric inhibitor-resistant mutation.
  • Example Embodiment I-25a The method of Example Embodiment I-24, wherein the allosteric inhibitor-resistant mutation is selected from the group consisting of E76K, P491S, S502P, and a combination thereof.
  • Example Embodiment I-25b The method of Example Embodiment I-24, wherein the allosteric inhibitor-resistant mutation is selected from the group consisting of E76K and P491S
  • Example Embodiment I-26 The method of Example Embodiment I-24, wherein the allosteric inhibitor-resistant mutation is S502P.
  • Example Embodiment I-27 The method of any one of Example Embodiments I-24 to I-26, wherein the allosteric SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an allosteric SHP2 inhibitor compound of any one of Formula I, of Formula II, of Formula III, of Formula I-V1, of Formula I-V2, of Formula I-W, of Formula I-X, of Formula I-Y, of Formula I-Z, of Formula IV, of Formula V, of Formula VI, of Formula IV-X, of Formula IV-Y, of Formula IV-Z, of Formula VII, of Formula VIII, of Formula IX, and of Formula X; (vi) TNO155, and (vii) a combination thereof.
  • the allosteric SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) Compound C; (iv) SHP099; (v) an all
  • Example Embodiment I-28 The method of any one of Example Embodiments I-24 through I-27, wherein the allosteric SHP2 inhibitor is in an effective amount.
  • Example Embodiment I-29 A diagnostic test for allosteric SHP2 inhibitor sensitivity, comprising a nucleic acid probe specific for an allosteric inhibitor-sensitive mutation of SHP2.
  • Example Embodiment I-29a An in vitro diagnostic test for allosteric SHP2 inhibitor sensitivity, comprising a nucleic acid probe specific for an allosteric inhibitor-sensitive mutation of SHP2.
  • Example Embodiment I-30 The diagnostic test of Example Embodiment I-29, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, S189A, D61G, E69K, T73I, Q506P, and a combination thereof.
  • Example Embodiment I-31 The diagnostic test of Example Embodiment I-29, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of F285S, L262R, and S189A.
  • Example Embodiment I-32 The diagnostic test of Example Embodiment I-29, wherein the allosteric inhibitor-sensitive mutation is D61G.
  • Example Embodiment I-33 The diagnostic test of Example Embodiment I-29, wherein the allosteric inhibitor-sensitive mutation is selected from the group consisting of E69K, T73I, and Q506P.
  • Example Embodiment I-34 A diagnostic test for allosteric SHP2 inhibitor insensitivity, comprising a nucleic acid probe specific for a SHP2 allosteric inhibitor-resistant mutation; wherein the allosteric inhibitor-resistant mutation is optionally selected from E76K, P491S, S502P.
  • SHP2 (PTPN11) is a non-receptor protein tyrosine phosphatase and scaffold protein that functions downstream of multiple RTKs, integrating growth factor signals to promote RAS/MAPK activation.
  • SHP2 is composed of three distinct structural domains: two SH2 domains at the N-terminus followed by a PTP catalytic domain. SHP2 adopts an autoinhibited conformation in the absence of RTK signaling. Mutations that destabilize the autoinhibited conformation are common in inherited RASopathies and certain cancers.
  • Allosteric inhibitors that stabilize the autoinhibited conformation in wild-type SHP2 inhibit RAS/MAPK signaling, and tumor growth, in xenograft models driven by oncogenic mutations in the RAS/MAPK pathway. This study asked what is the effect of allosteric inhibitors on activated mutant SHP2.
  • SHP2 can be activated in vitro by synthetic peptides containing diphosphotyrosine motifs. Mutations in the SH2-Catalytic domain interface can uncouple activation from phosphotyrosine peptide or protein binding. Molecules that bind specifically to the autoinhibited conformation function as allosteric inhibitors
  • the present study examined the effect of allosteric inhibitors on mutant SHP2s.
  • the following mutations associated with Noonan Syndrome, Juvenile Myelomonocytic Leukemia (JMML), and other human cancers were selected for further experimental study: D61G, E76K, S189A, L262R, F285S, P491S and S502P. Mutations refer to the SHP2 sequence numbered according to Uniprot Isoform 2 (accession number Q06124-2) (SEQ ID NO: 1).
  • SHP2 Full-length SHP2 is allosterically activated through binding of bis-tyrosyl-phorphorylated peptides to its Src Homology 2 (SH2) domains.
  • SH2 Src Homology 2
  • the latter activation step leads to the release of the auto-inhibitory interface of SHP2, which in turn renders the SHP2 protein tyrosine phosphatase (PTP) active and available for substrate recognition and reaction catalysis.
  • PTP protein tyrosine phosphatase
  • the catalytic activity of SHP2 was monitored using the surrogate substrate DiFMUP in a prompt fluorescence assay format. Mutant variants of SHP2 showed variable response to activating peptide, and the biochemical assay was repeated on all enzymes with and without activating peptide at a concentration of 500 nM.
  • the phosphatase reactions were performed at room temperature in 384-well black polystyrene plates, flat bottom, non-binding surface (Corning, Cat #781077) using a final reaction volume of 50 ⁇ L and the following assay buffer conditions: 55 mM HEPES pH 7.2, 100 mM NaCl, 0.5 mM EDTA, 1 mM DTT, 0.001% Brij35, 0.002% BSA, 0.1% DMSO, 100 ⁇ M DiFMUP, 0.1, 0.3, or 2 nM enzyme, 0 or 500 nM activating peptide NsCs and 10 ⁇ M to 1.9 ⁇ M inhibitor.
  • Diluted inhibitor (5 ⁇ L) was mixed with activated enzyme (25 ⁇ l) and incubated for 30 minutes at room temperature.
  • 50 ⁇ l stop solution (0.1 mM sodium pervanadate) was added to each well, the plate was shaken briefly to mix, and read in endpoint mode on a SpectraMax M5 plate reader (Molecular Devices) using excitation and emission wavelengths of 340 nm and 450 nm. Data was imported into GraphPad Prism. Plots of fluorescence intensity vs. log Molar [compound] were created and modeled with a 3-parameter sigmoidal concentration response equation in order to estimate IC 50 .
  • Compound C also known as Compound 33 on Tables 1-8) and 52 other allosteric inhibitors of SHP2 were tested for their potency in a biochemical assay of SHP2 activity.
  • wildtype or mutant variants of SHP2 were incubated with each of compounds 1-53 for 30 minutes, prior to addition of the small molecule substrate DiFMUP (6,8-difluoro-4-methylumbelliferyl phosphate). Reactions were then allowed to proceed for 30 minutes and stopped by the addition of a phosphatase inhibitor, sodium pervanadate. De-phosphorylation of DiFMUP results in production of a fluorescent product. Product fluorescence was determined and plotted as a function of compound concentration in order to determine the IC 50 for each compound on each mutant using a four parameter sigmoidal dose response function in Prism (GraphPad).
  • NsCs bis-phosphorylated activating peptide
  • the experiments were repeated in the presence of a bis-phosphorylated activating peptide (termed “NsCs”) which comprises two tyrosine phosphorylated 9-mers (synthetic sequences designed to strongly bind both the N- and C-terminal SH2 domains) connected by a PEG8 linker.
  • NsCs mimics the role of the cytosolic domain of a protein tyrosine kinase in this model system.
  • the NsCs activating peptide has the following structure:
  • the potencies of 52 compounds to inhibit the non-activated (apo) and activated forms of the various mutants, in comparison to the wild type SHP2, are summarized in Tables 1 to 8.
  • the potency of each compound to inhibit non-activated mutant SHP2 is plotted versus the potency to inhibit wild-type SHP2 in FIG. 2 .
  • the same plot for activated mutant and wild-type SHP2 is shown in FIG. 3 .
  • mutations show a peptide-driven shift in inhibitor potency of varying magnitude.
  • the peptide shifted IC 50 values 3-fold or less for S189A and F285S.
  • S502P exhibited a peptide-driven potency shift of at least 100-fold, but the exact shift could not be determined because no inhibitory activity was detected for any compound (up to the highest test concentration of 10 ⁇ M) in the presence of activating peptide.
  • the shift for S189A, F285S, D61G, and E76K are shown in FIG. 5 .
  • the Flp-In T-REx-293 cell line was obtained from Gibco® and cultivated in high glucose DMEMTM containing 2 mM L-glutamine (Hyclone®), supplemented with 10% FBS (Hyclone®), 1% penicillin/streptomycin (Gibco®), 100 ⁇ g/mL ZeocinTM (Gibco®), and 15 ⁇ g/mL blasticidin (Gibco®) in a humidified cell culture incubator at 37° C., 5% CO2.
  • Wild type or mutant SHP2 variants were synthesized and subcloned into the pcDNA5/FRT/TO vector (ThermoFisher). Plasmids were co-transfected with the pOG44 Flp recombinase expression plasmid (ThermoFisher®) into Flp-In T-REx-293 cells using X-tremegene 9 DNA transfection reagent (Sigma®), according to the manufacturer's instructions.
  • Cells that underwent successful recombination were selected in high glucose DMEM containing 2 mM L-glutamine, supplemented with 10% FBS and, 1% penicillin/streptomycin, 200 ⁇ g/mL hygromycin B (Gibco®), and 15 ⁇ g/mL blasticidin (Gibco®) (recombinant selection media) in a humidified cell culture incubator at 37° C., 5% CO2, until colonies were visually discernible. Colonies were expanded in recombinant selection media in a humidified cell culture incubator at 37° C., 5% CO2 to establish isogenic SHP2 variant expression cell lines (T-REx-293-SHP2).
  • T-REx-293-SHP2 cells for each tested variant were harvested and seeded in high glucose DMEM containing 2 mM L-glutamine, supplemented with 0.1% FBS and, 1% penicillin/streptomycin, 200 ⁇ g/mL hygromycin B, and 15 ⁇ g/mL blasticidin in 96-well assay plates at a density of 25,000 cells/well.
  • ERK1/2 phosphorylation at Thr202/Tyr204 was assayed using the AlphaLISA SureFire Ultra HV pERK Assay Kit (Perkin Elmer®) following the manufacturer's instructions. Samples were read using an EnVision Multilabel Plate Reader (Perkin Elmer®) using standard AlphaLISA settings. Assay data was plotted and EC50 values were determined using four-parameter concentration-response model in GraphPad Prism 7. Data provided are mean+/ ⁇ standard deviation of duplicate values from representative experiments.

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